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rLAMMPS lammps
compute_rigid_local.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include "compute_rigid_local.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "fix_rigid_small.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
enum
{
ID
,
MOL
,
MASS
,
X
,
Y
,
Z
,
XU
,
YU
,
ZU
,
VX
,
VY
,
VZ
,
FX
,
FY
,
FZ
,
IX
,
IY
,
IZ
,
TQX
,
TQY
,
TQZ
,
OMEGAX
,
OMEGAY
,
OMEGAZ
,
ANGMOMX
,
ANGMOMY
,
ANGMOMZ
,
QUATW
,
QUATI
,
QUATJ
,
QUATK
,
INERTIAX
,
INERTIAY
,
INERTIAZ
};
/* ---------------------------------------------------------------------- */
ComputeRigidLocal
::
ComputeRigidLocal
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
5
)
error
->
all
(
FLERR
,
"Illegal compute rigid/local command"
);
local_flag
=
1
;
nvalues
=
narg
-
4
;
if
(
nvalues
==
1
)
size_local_cols
=
0
;
else
size_local_cols
=
nvalues
;
int
n
=
strlen
(
arg
[
3
])
+
1
;
idrigid
=
new
char
[
n
];
strcpy
(
idrigid
,
arg
[
3
]);
rstyle
=
new
int
[
nvalues
];
nvalues
=
0
;
for
(
int
iarg
=
4
;
iarg
<
narg
;
iarg
++
)
{
if
(
strcmp
(
arg
[
iarg
],
"id"
)
==
0
)
rstyle
[
nvalues
++
]
=
ID
;
else
if
(
strcmp
(
arg
[
iarg
],
"mol"
)
==
0
)
rstyle
[
nvalues
++
]
=
MOL
;
else
if
(
strcmp
(
arg
[
iarg
],
"mass"
)
==
0
)
rstyle
[
nvalues
++
]
=
MASS
;
else
if
(
strcmp
(
arg
[
iarg
],
"x"
)
==
0
)
rstyle
[
nvalues
++
]
=
X
;
else
if
(
strcmp
(
arg
[
iarg
],
"y"
)
==
0
)
rstyle
[
nvalues
++
]
=
Y
;
else
if
(
strcmp
(
arg
[
iarg
],
"z"
)
==
0
)
rstyle
[
nvalues
++
]
=
Z
;
else
if
(
strcmp
(
arg
[
iarg
],
"xu"
)
==
0
)
rstyle
[
nvalues
++
]
=
XU
;
else
if
(
strcmp
(
arg
[
iarg
],
"yu"
)
==
0
)
rstyle
[
nvalues
++
]
=
YU
;
else
if
(
strcmp
(
arg
[
iarg
],
"zu"
)
==
0
)
rstyle
[
nvalues
++
]
=
ZU
;
else
if
(
strcmp
(
arg
[
iarg
],
"vx"
)
==
0
)
rstyle
[
nvalues
++
]
=
VX
;
else
if
(
strcmp
(
arg
[
iarg
],
"vy"
)
==
0
)
rstyle
[
nvalues
++
]
=
VY
;
else
if
(
strcmp
(
arg
[
iarg
],
"vz"
)
==
0
)
rstyle
[
nvalues
++
]
=
VZ
;
else
if
(
strcmp
(
arg
[
iarg
],
"fx"
)
==
0
)
rstyle
[
nvalues
++
]
=
FX
;
else
if
(
strcmp
(
arg
[
iarg
],
"fy"
)
==
0
)
rstyle
[
nvalues
++
]
=
FY
;
else
if
(
strcmp
(
arg
[
iarg
],
"fz"
)
==
0
)
rstyle
[
nvalues
++
]
=
FZ
;
else
if
(
strcmp
(
arg
[
iarg
],
"ix"
)
==
0
)
rstyle
[
nvalues
++
]
=
IX
;
else
if
(
strcmp
(
arg
[
iarg
],
"iy"
)
==
0
)
rstyle
[
nvalues
++
]
=
IY
;
else
if
(
strcmp
(
arg
[
iarg
],
"iz"
)
==
0
)
rstyle
[
nvalues
++
]
=
IZ
;
else
if
(
strcmp
(
arg
[
iarg
],
"tqx"
)
==
0
)
rstyle
[
nvalues
++
]
=
TQX
;
else
if
(
strcmp
(
arg
[
iarg
],
"tqy"
)
==
0
)
rstyle
[
nvalues
++
]
=
TQY
;
else
if
(
strcmp
(
arg
[
iarg
],
"tqz"
)
==
0
)
rstyle
[
nvalues
++
]
=
TQZ
;
else
if
(
strcmp
(
arg
[
iarg
],
"omegax"
)
==
0
)
rstyle
[
nvalues
++
]
=
OMEGAX
;
else
if
(
strcmp
(
arg
[
iarg
],
"omegay"
)
==
0
)
rstyle
[
nvalues
++
]
=
OMEGAY
;
else
if
(
strcmp
(
arg
[
iarg
],
"omegaz"
)
==
0
)
rstyle
[
nvalues
++
]
=
OMEGAZ
;
else
if
(
strcmp
(
arg
[
iarg
],
"angmomx"
)
==
0
)
rstyle
[
nvalues
++
]
=
ANGMOMX
;
else
if
(
strcmp
(
arg
[
iarg
],
"angmomy"
)
==
0
)
rstyle
[
nvalues
++
]
=
ANGMOMY
;
else
if
(
strcmp
(
arg
[
iarg
],
"angmomz"
)
==
0
)
rstyle
[
nvalues
++
]
=
ANGMOMZ
;
else
if
(
strcmp
(
arg
[
iarg
],
"quatw"
)
==
0
)
rstyle
[
nvalues
++
]
=
QUATW
;
else
if
(
strcmp
(
arg
[
iarg
],
"quati"
)
==
0
)
rstyle
[
nvalues
++
]
=
QUATI
;
else
if
(
strcmp
(
arg
[
iarg
],
"quatj"
)
==
0
)
rstyle
[
nvalues
++
]
=
QUATJ
;
else
if
(
strcmp
(
arg
[
iarg
],
"quatk"
)
==
0
)
rstyle
[
nvalues
++
]
=
QUATK
;
else
if
(
strcmp
(
arg
[
iarg
],
"inertiax"
)
==
0
)
rstyle
[
nvalues
++
]
=
INERTIAX
;
else
if
(
strcmp
(
arg
[
iarg
],
"inertiay"
)
==
0
)
rstyle
[
nvalues
++
]
=
INERTIAY
;
else
if
(
strcmp
(
arg
[
iarg
],
"inertiaz"
)
==
0
)
rstyle
[
nvalues
++
]
=
INERTIAZ
;
else
error
->
all
(
FLERR
,
"Invalid keyword in compute rigid/local command"
);
}
ncount
=
nmax
=
0
;
vector
=
NULL
;
array
=
NULL
;
fixrigid
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputeRigidLocal
::~
ComputeRigidLocal
()
{
memory
->
destroy
(
vector
);
memory
->
destroy
(
array
);
delete
[]
idrigid
;
delete
[]
rstyle
;
}
/* ---------------------------------------------------------------------- */
void
ComputeRigidLocal
::
init
()
{
// set fixrigid
int
ifix
=
modify
->
find_fix
(
idrigid
);
if
(
ifix
<
0
)
error
->
all
(
FLERR
,
"FixRigidSmall ID for compute rigid/local does not exist"
);
fixrigid
=
(
FixRigidSmall
*
)
modify
->
fix
[
ifix
];
int
flag
=
0
;
if
(
strstr
(
fixrigid
->
style
,
"rigid/"
)
==
NULL
)
flag
=
1
;
if
(
strstr
(
fixrigid
->
style
,
"/small"
)
==
NULL
)
flag
=
1
;
if
(
flag
)
error
->
all
(
FLERR
,
"Compute rigid/local does not use fix rigid/small fix"
);
// do initial memory allocation so that memory_usage() is correct
ncount
=
compute_rigid
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
}
/* ---------------------------------------------------------------------- */
void
ComputeRigidLocal
::
compute_local
()
{
invoked_local
=
update
->
ntimestep
;
// count local entries and compute bond info
ncount
=
compute_rigid
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
ncount
=
compute_rigid
(
1
);
}
/* ----------------------------------------------------------------------
count rigid bodies and compute rigid info on this proc
if flag is set, compute requested info about rigid body
owning atom of rigid body must be in group
------------------------------------------------------------------------- */
int
ComputeRigidLocal
::
compute_rigid
(
int
flag
)
{
int
i
,
m
,
n
,
ibody
;
double
*
ptr
;
FixRigidSmall
::
Body
*
body
;
double
xprd
=
domain
->
xprd
;
double
yprd
=
domain
->
yprd
;
double
zprd
=
domain
->
zprd
;
tagint
*
tag
=
atom
->
tag
;
tagint
*
molecule
=
atom
->
molecule
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
m
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
!
(
mask
[
i
]
&
groupbit
))
continue
;
ibody
=
fixrigid
->
bodyown
[
i
];
if
(
ibody
<
0
)
continue
;
body
=
&
fixrigid
->
body
[
ibody
];
if
(
flag
)
{
if
(
nvalues
==
1
)
ptr
=
&
vector
[
m
];
else
ptr
=
array
[
m
];
for
(
n
=
0
;
n
<
nvalues
;
n
++
)
{
switch
(
rstyle
[
n
])
{
case
ID:
ptr
[
n
]
=
tag
[
body
->
ilocal
];
break
;
case
MOL:
ptr
[
n
]
=
molecule
[
body
->
ilocal
];
break
;
case
MASS:
ptr
[
n
]
=
body
->
mass
;
break
;
case
X:
ptr
[
n
]
=
body
->
xcm
[
0
];
break
;
case
Y:
ptr
[
n
]
=
body
->
xcm
[
1
];
break
;
case
Z:
ptr
[
n
]
=
body
->
xcm
[
2
];
break
;
case
XU:
ptr
[
n
]
=
body
->
xcm
[
0
]
+
((
body
->
image
&
IMGMASK
)
-
IMGMAX
)
*
xprd
;
break
;
case
YU:
ptr
[
n
]
=
body
->
xcm
[
1
]
+
((
body
->
image
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
)
*
yprd
;
break
;
case
ZU:
ptr
[
n
]
=
body
->
xcm
[
2
]
+
((
body
->
image
>>
IMG2BITS
)
-
IMGMAX
)
*
zprd
;
break
;
case
VX:
ptr
[
n
]
=
body
->
vcm
[
0
];
break
;
case
VY:
ptr
[
n
]
=
body
->
vcm
[
1
];
break
;
case
VZ:
ptr
[
n
]
=
body
->
vcm
[
2
];
break
;
case
FX:
ptr
[
n
]
=
body
->
fcm
[
0
];
break
;
case
FY:
ptr
[
n
]
=
body
->
fcm
[
1
];
break
;
case
FZ:
ptr
[
n
]
=
body
->
fcm
[
2
];
break
;
case
IX:
ptr
[
n
]
=
(
body
->
image
&
IMGMASK
)
-
IMGMAX
;
break
;
case
IY:
ptr
[
n
]
=
(
body
->
image
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
break
;
case
IZ:
ptr
[
n
]
=
(
body
->
image
>>
IMG2BITS
)
-
IMGMAX
;
break
;
case
TQX:
ptr
[
n
]
=
body
->
torque
[
0
];
break
;
case
TQY:
ptr
[
n
]
=
body
->
torque
[
1
];
break
;
case
TQZ:
ptr
[
n
]
=
body
->
torque
[
2
];
break
;
case
OMEGAX:
ptr
[
n
]
=
body
->
omega
[
0
];
break
;
case
OMEGAY:
ptr
[
n
]
=
body
->
omega
[
1
];
break
;
case
OMEGAZ:
ptr
[
n
]
=
body
->
omega
[
2
];
break
;
case
ANGMOMX:
ptr
[
n
]
=
body
->
angmom
[
0
];
break
;
case
ANGMOMY:
ptr
[
n
]
=
body
->
angmom
[
1
];
break
;
case
ANGMOMZ:
ptr
[
n
]
=
body
->
angmom
[
2
];
break
;
case
QUATW:
ptr
[
n
]
=
body
->
quat
[
0
];
break
;
case
QUATI:
ptr
[
n
]
=
body
->
quat
[
1
];
break
;
case
QUATJ:
ptr
[
n
]
=
body
->
quat
[
2
];
break
;
case
QUATK:
ptr
[
n
]
=
body
->
quat
[
3
];
break
;
case
INERTIAX:
ptr
[
n
]
=
body
->
inertia
[
0
];
break
;
case
INERTIAY:
ptr
[
n
]
=
body
->
inertia
[
1
];
break
;
case
INERTIAZ:
ptr
[
n
]
=
body
->
inertia
[
2
];
break
;
}
}
}
m
++
;
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
ComputeRigidLocal
::
reallocate
(
int
n
)
{
// grow vector or array
while
(
nmax
<
n
)
nmax
+=
DELTA
;
if
(
nvalues
==
1
)
{
memory
->
destroy
(
vector
);
memory
->
create
(
vector
,
nmax
,
"rigid/local:vector"
);
vector_local
=
vector
;
}
else
{
memory
->
destroy
(
array
);
memory
->
create
(
array
,
nmax
,
nvalues
,
"rigid/local:array"
);
array_local
=
array
;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeRigidLocal
::
memory_usage
()
{
double
bytes
=
nmax
*
nvalues
*
sizeof
(
double
);
return
bytes
;
}
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